The two most likely things are that the database on the device has become corrupted, or the setting in the KoboTouch driver in calibre have changed.
Depending on the settings, the driver maintains the collections each time the device is connected. If you change the settings you will get different collections. And as the collections are based on columns in the library, changes to the metadata in the library will affect the collections. You should check the setting are still what you want and the confirm that the columns you are using for the collections still contain the expected values.
If it is the database, you will need to fix that either by restoring a backup of the database, or by signing out. Unfortunately, the latter will lose your reading status. As you are using calibre, you can use my Kobo Utilities plugin to store the reading status and then restore them later.
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